fix: clarify code navigation freshness and exact-path errors

[jlitola]

Summary

• stop rendering obsolete ref suggestions after a waited search reaches the requested commit
• promote FILE_PATH_EXCLUDED and SOURCE_FILE_INVENTORY_UNKNOWN to stable CLI/MCP error codes while preserving backend metadata
• add surface-native recovery guidance across CLI terminal, CLI JSON, MCP read, and MCP grep flows
• align tool descriptions, CLI help, implementation docs, parity coverage, and release fragments

Validation

• bun test — 2,785 passed, 0 failed
• final focused suite — 189 passed, 0 failed
• bun run typecheck
• bun run format:check
• bun run lint
• bun run build
• bun run validate:packages
• bun run plugins:generate && bun run plugins:check
• authenticated bun run smoke:cli — 78 steps
• authenticated bun run smoke:mcp — 38 steps
• built unauthenticated CLI and MCP smokes
• targeted Codex MCP agent eval — high confidence, no tool or instruction issues
• Claude Opus review loop — final pass clean with no findings

Closes #282
Closes #284